I have much experience rebuilding these roofs and have been trained by BMW to service them.

If you are new to your X3 and don't know much about the roof then I can give you a few hints to help maintain it / do and don'ts

Take a close look at the moving plastic rail mechanisms, and check for micro cracks. These cracks will eventually get worse and cause failure. Another defiantly don't do is... DO NOT continue to command the roof in any direction if you hear loud cracking or popping from the switch area aka. FZD, STOP! When you hear this popping it is the motor skipping on the drive cables and getting further and further out of time. When these roofs are out of time I have seen them flex and shatter the glass panels!

Cleaning the roof channels should be done too. BMW actually has a special tool that I use for the channel cleaning.
You can use a soft cloth and something to force it into the channels. As far as lube, they have a special grease too. They do offer it in small packets, and I am told this is the only type of grease you should use. When you apply it only apply a FILM.

Roof drains in the front run down the A-pillar and exit under neath just under the front doors closer to the front. They have closed end to keep debris out and prevent clogging, but instead it does the opposite. When you clean the drain, be sure to open this closed end and essentially finger the hole to be sure it is clear. During cleaning it is a good idea to check drain flow rate by pouring water into the water channel( outer most channel). You may see dirt actually puke out of the front drains. You can tell a free flowing drain by the sound it makes when draining...the Venturi effect creates a suction sound, and if you don't hear it, it's not flowing well. Usually this is all you have to do for the front drains.
Rear drains you will not find the exit until you remove the bumper cover. The way I clear them is
1 remove d-pillar trim.
2 take the top half of the trunk seal off
3 At the center of the headliner gently pull down and look for a plastic clip that is inserted into the roof. Take notice to the way it is held into the headliner. The plastic clip stays with the headliner!! It will break!! I use a long panel popper to remove if from the metal roof. Once it is loose there is quite a bit of play. It gets a little tight but I find the rear of the cassette and remove the drains and gentlly clear them with compressed air. The headliner is pretty resilient so if you see it creasing, it goes back to normal once back in place. WITHIN REASON!

There is a calibration for the roof aka. Sunroof initialization. Try and do this when the roof is closed if possible. Push the sunroof button straight up and hold for the whole procedure. The roof runs through all positions starting with vent ( if the sunshade is closed it also runs the slit shade position at this time) then runs the shade open, then glass open to close, the shade closed. Only release the button once movement has completely stopped!! The FZD learns all end stops and this calibration is essential for the one touch feature and anti-trap function.